Mount Sinai researchers create smart tweezers that can isolate single bacteria from microbiome samples before genetic sequencing

New technology could allow genetic scientists to identify antibiotic resistance genes and help doctors choose better treatments for genetic diseases

Genomic scientists at the Icahn School of Medicine at Mount Sinai Medical Center in New York City have developed what they call smart tweezers that allow researchers to isolate single bacteria from a patient’s microbiome in preparation for genetic sequencing. While this new technology is primarily intended for research purposes, it could one day be used by clinical laboratories and microbiologists to help doctors diagnose chronic diseases and select appropriate gene therapies.

Researchers designed a new technology called mEnrich-seq to improve the efficiency of studying complex microbial communities in the human microbiome. According to a press release from Mount Sinai Hospital, the discovery ushered in a new era of precise microbiome research.

Metagenomics enables comprehensive studies of the microbiome. However, many applications would benefit from methods that sequence specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (where m stands for methylation and seq stands for sequencing) to enrich genes of interest from metagenomic DNA before sequencing, the scientists wrote in a paper published in Nature. taxon. natural method Titled mEnrich-seq: Methylation-guided enrichment sequencing of bacterial taxa of interest in the microbiome.

Addressing technology gaps in genetic research

Any imbalance or reduction in the variety of microorganisms in the body can lead to an increased risk of illness and disease.

For example, imbalances in the normal gut microbiome are associated with conditions such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), obesity, type 2 diabetes, and allergies. At the same time, the vaginal microbiome appears to influence sexual and reproductive health, Inside Precision Medicine famous.

When studying the microbiome, many scientists focus on studying specific types of bacteria in a sample rather than studying every bacterial type present, the release said. The limitation of this approach is that a specific bacterium is only part of a complex environment that includes other bacteria, viruses, fungi and host cells, each with its own unique DNA.

According to the press release, mEnrich-seq works by taking advantage of the codes written on bacterial DNA, which bacteria naturally use to distinguish one from another as part of their natural immune system. This new strategy addresses a critical technology gap, as previously researchers needed to isolate specific strains of bacteria from a given sample using media that selectively culture them, a time-consuming process that works for some bacteria. But not for other bacteria. In contrast, mEnrich-seq can recover the genomes of bacteria of interest directly from microbiome samples, without the need for culture.

Isolate difficult-to-culture bacteria

To conduct their study, Icahn researchers used mEnrich-seq to analyze urine samples from three patients with urinary tract infections (UTIs) to reconstruct E. coli (E. coli)Genome. They found that their smart tweezers covered more than 99.97% of the genome in all samples. This facilitates a comprehensive examination of antibiotic resistance genes in each genome. They found that mEnrich-seq had better sensitivity than standard methods for studying the urine microbiome.

They also used mEnrich-seq to selectively examine genomes Akkermansia muciniphila (Acidobacter muciniphila), a bacterium that colonizes the gut and has been shown to respond to obesity and type 2 diabetes, as well as to cancer immunotherapy.

Akkermansia Fang tells us that cultivating culture is very difficult Genome Network. Cultivating it takes several weeks and requires special equipment and special expertise. Very boring.

mEnrich-seq can quickly convert it from more than 99.7% Acidobacter muciniphila Genomes in the sample.

Combating global antibiotic resistance

According to the press release, mEnrich-seq may benefit future microbiome research because:

• Cost-effectiveness: It provides a more economical approach to microbiome research and is particularly beneficial for large-scale studies where resources may be limited.
• Wide applicability: This method can focus on a variety of bacteria, making it a versatile tool for research and clinical applications.
• medical breakthrough: By enabling more targeted research, mEnrich-seq can accelerate the development of new diagnostic tools and treatments.

One of the most exciting aspects of mEnrich-seq is its potential to uncover previously missed details, such as antibiotic resistance genes that traditional sequencing methods have been unable to detect due to a lack of sensitivity, Fang said in a press release. This could be an important step towards solving the global problem of antibiotic resistance.

More research and clinical trials are needed before mEnrich-seq can be used in medicine. The Icahn researchers plan to refine their new genetic tool to increase its efficiency and expand its applications. They also intend to work with doctors and other healthcare professionals to validate how it can be used in clinical settings.

If this becomes a reality, hospital infection control teams, clinical laboratories and microbiology laboratories will welcome a technology that improves their ability to detect details such as antibiotic resistance genes, allowing faster and more accurate diagnosis of patient infections . This, in turn, may help improve patient outcomes.

JP Schlingman

relevant information:

Smart tweezers can remove single bacterial targets from the microbiome

mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest in the microbiome

Genomic tweezers usher in new era of precision in microbiome research

Molecular tweezers enable precise selection of microbiome bacteria

Identification of DNA motifs that regulate DNA methylation

New bacterial epigenetic sequencing method may benefit complex microbiome analysis